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Nat Genet. 2016 Aug;48(8):927-34. doi: 10.1038/ng.3596. Epub 2016 Jun 20.

Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice.

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Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.
NARO Institute of Vegetable and Tea Science, Tsu, Japan.
Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo, Japan.
Hyogo Prefectural Research Center for Agriculture, Forestry and Fisheries, Kasai, Hyogo, Japan.


A genome-wide association study (GWAS) can be a powerful tool for the identification of genes associated with agronomic traits in crop species, but it is often hindered by population structure and the large extent of linkage disequilibrium. In this study, we identified agronomically important genes in rice using GWAS based on whole-genome sequencing, followed by the screening of candidate genes based on the estimated effect of nucleotide polymorphisms. Using this approach, we identified four new genes associated with agronomic traits. Some genes were undetectable by standard SNP analysis, but we detected them using gene-based association analysis. This study provides fundamental insights relevant to the rapid identification of genes associated with agronomic traits using GWAS and will accelerate future efforts aimed at crop improvement.

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